A citation-based method for searching scientific literature

Karthik Arumugam, William Shin, Valentina Schiavone, Lukas Vlahos, Xiaochuan Tu, Davide Carnevali, Jordan Kesner, Evan O Paull, Neus Romo, Prem Subramaniam, Jeremy Worley, Xiangtian Tan, Andrea Califano, Maria Pia Cosma. Cell Rep 2020
Times Cited: 1







List of co-cited articles
articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
628
100

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
100

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis.
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir,[...]. Lancet Oncol 2017
372
100

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.
Hongxu Ding, Eugene F Douglass, Adam M Sonabend, Angeliki Mela, Sayantan Bose, Christian Gonzalez, Peter D Canoll, Peter A Sims, Mariano J Alvarez, Andrea Califano. Nat Commun 2018
27
100


CD70 expression patterns in renal cell carcinoma.
Lucia B Jilaveanu, Joshua Sznol, Saadia A Aziz, Dylan Duchen, Harriet M Kluger, Robert L Camp. Hum Pathol 2012
28
100

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.
Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki,[...]. Nucleic Acids Res 2019
46
100

Reverse engineering of regulatory networks in human B cells.
Katia Basso, Adam A Margolin, Gustavo Stolovitzky, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano. Nat Genet 2005
844
100

TREM-2 serves as a negative immune regulator through Syk pathway in an IL-10 dependent manner in lung cancer.
Yinan Yao, Hequan Li, Junjun Chen, Weiyi Xu, Guangdie Yang, Zhang Bao, Dajing Xia, Guohua Lu, Shuwen Hu, Jianying Zhou. Oncotarget 2016
15
100

A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.
Mariano J Alvarez, Prem S Subramaniam, Laura H Tang, Adina Grunn, Mahalaxmi Aburi, Gabrielle Rieckhof, Elena V Komissarova, Elizabeth A Hagan, Lisa Bodei, Paul A Clemons,[...]. Nat Genet 2018
57
100

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.
Yasin Şenbabaoğlu, Ron S Gejman, Andrew G Winer, Ming Liu, Eliezer M Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna,[...]. Genome Biol 2016
287
100

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
575
100

Prognostic and theranostic impact of molecular subtypes and immune classifications in renal cell cancer (RCC) and colorectal cancer (CRC).
Etienne Becht, Nicolas A Giraldo, Benoit Beuselinck, Sylvie Job, Laetitia Marisa, Yann Vano, Stéphane Oudard, Jessica Zucman-Rossi, Pierre Laurent-Puig, Catherine Sautès-Fridman,[...]. Oncoimmunology 2015
26
100

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.
Ela Elyada, Mohan Bolisetty, Pasquale Laise, William F Flynn, Elise T Courtois, Richard A Burkhart, Jonathan A Teinor, Pascal Belleau, Giulia Biffi, Matthew S Lucito,[...]. Cancer Discov 2019
260
100

Tumor Cells Hijack Macrophage-Produced Complement C1q to Promote Tumor Growth.
Lubka T Roumenina, Marie V Daugan, Rémi Noé, Florent Petitprez, Yann A Vano, Rafaël Sanchez-Salas, Etienne Becht, Julie Meilleroux, Bénédicte Le Clec'h, Nicolas A Giraldo,[...]. Cancer Immunol Res 2019
43
100

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer.
Woosung Chung, Hye Hyeon Eum, Hae-Ock Lee, Kyung-Min Lee, Han-Byoel Lee, Kyu-Tae Kim, Han Suk Ryu, Sangmin Kim, Jeong Eon Lee, Yeon Hee Park,[...]. Nat Commun 2017
315
100

BLUEPRINT: mapping human blood cell epigenomes.
Joost H A Martens, Hendrik G Stunnenberg. Haematologica 2013
81
100

TOX is a critical regulator of tumour-specific T cell differentiation.
Andrew C Scott, Friederike Dündar, Paul Zumbo, Smita S Chandran, Christopher A Klebanoff, Mojdeh Shakiba, Prerak Trivedi, Laura Menocal, Heather Appleby, Steven Camara,[...]. Nature 2019
233
100

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas.
Kartik M Mani, Celine Lefebvre, Kai Wang, Wei Keat Lim, Katia Basso, Riccardo Dalla-Favera, Andrea Califano. Mol Syst Biol 2008
151
100

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion.
Omar Khan, Josephine R Giles, Sierra McDonald, Sasikanth Manne, Shin Foong Ngiow, Kunal P Patel, Michael T Werner, Alexander C Huang, Katherine A Alexander, Jennifer E Wu,[...]. Nature 2019
289
100

CD70: An emerging target in cancer immunotherapy.
J Jacobs, V Deschoolmeester, K Zwaenepoel, C Rolfo, K Silence, S Rottey, F Lardon, E Smits, P Pauwels. Pharmacol Ther 2015
47
100

Systemic treatment of renal cell cancer: A comprehensive review.
Amparo Sánchez-Gastaldo, Emmanuelle Kempf, Aránzazu González Del Alba, Ignacio Duran. Cancer Treat Rev 2017
53
100

An Immune Atlas of Clear Cell Renal Cell Carcinoma.
Stéphane Chevrier, Jacob Harrison Levine, Vito Riccardo Tomaso Zanotelli, Karina Silina, Daniel Schulz, Marina Bacac, Carola Hermine Ries, Laurie Ailles, Michael Alexander Spencer Jewett, Holger Moch,[...]. Cell 2017
386
100

CD24 signalling through macrophage Siglec-10 is a target for cancer immunotherapy.
Amira A Barkal, Rachel E Brewer, Maxim Markovic, Mark Kowarsky, Sammy A Barkal, Balyn W Zaro, Venkatesh Krishnan, Jason Hatakeyama, Oliver Dorigo, Layla J Barkal,[...]. Nature 2019
207
100

Renal cell carcinoma: the search for a reliable biomarker.
Nicholas J Farber, Christopher J Kim, Parth K Modi, Jane D Hon, Evita T Sadimin, Eric A Singer. Transl Cancer Res 2017
38
100

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Livnat Jerby-Arnon, Parin Shah, Michael S Cuoco, Christopher Rodman, Mei-Ju Su, Johannes C Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin,[...]. Cell 2018
297
100

Unlocking the Complexities of Tumor-Associated Regulatory T Cells.
Jaime L Chao, Peter A Savage. J Immunol 2018
30
100

Molecular aspects of renal cell carcinoma: a review.
Hari Koul, Jung-Sik Huh, Kyle O Rove, Luiza Crompton, Sweaty Koul, Randall B Meacham, Fernando J Kim. Am J Cancer Res 2011
65
100

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
100

KRT8 upregulation promotes tumor metastasis and is predictive of a poor prognosis in clear cell renal cell carcinoma.
Hai-Song Tan, Wei-Hua Jiang, Yi He, De-Sheng Wang, Zhen-Jie Wu, Deng-Shuang Wu, Li Gao, Yi Bao, Jia-Zi Shi, Bing Liu,[...]. Oncotarget 2017
15
100

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer.
Yonatan Katzenelenbogen, Fadi Sheban, Adam Yalin, Ido Yofe, Dmitry Svetlichnyy, Diego Adhemar Jaitin, Chamutal Bornstein, Adi Moshe, Hadas Keren-Shaul, Merav Cohen,[...]. Cell 2020
42
100

45
100

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.
Teresa Davoli, Hajime Uno, Eric C Wooten, Stephen J Elledge. Science 2017
444
100

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Alexander Lachmann, Federico M Giorgi, Gonzalo Lopez, Andrea Califano. Bioinformatics 2016
95
100

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
412
100

Prognostic value of CD44 expression in renal cell carcinoma: a systematic review and meta-analysis.
Xintao Li, Xin Ma, Luyao Chen, Liangyou Gu, Yu Zhang, Fan Zhang, Yun Ouyang, Yu Gao, Qingbo Huang, Xu Zhang. Sci Rep 2015
33
100

Functional characterization of somatic mutations in cancer using network-based inference of protein activity.
Mariano J Alvarez, Yao Shen, Federico M Giorgi, Alexander Lachmann, B Belinda Ding, B Hilda Ye, Andrea Califano. Nat Genet 2016
225
100

Fc-Optimized Anti-CD25 Depletes Tumor-Infiltrating Regulatory T Cells and Synergizes with PD-1 Blockade to Eradicate Established Tumors.
Frederick Arce Vargas, Andrew J S Furness, Isabelle Solomon, Kroopa Joshi, Leila Mekkaoui, Marta H Lesko, Enrique Miranda Rota, Rony Dahan, Andrew Georgiou, Anna Sledzinska,[...]. Immunity 2017
173
100

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
100

Prognostic Significance of CD24 in Clear Cell Renal Cell Carcinoma.
Deniz Arik, Cavit Can, Emine Dündar, Sare Kabukçuoğlu, Özgül Paşaoğlu. Pathol Oncol Res 2017
8
100

The transcriptional network for mesenchymal transformation of brain tumours.
Maria Stella Carro, Wei Keat Lim, Mariano Javier Alvarez, Robert J Bollo, Xudong Zhao, Evan Y Snyder, Erik P Sulman, Sandrine L Anne, Fiona Doetsch, Howard Colman,[...]. Nature 2010
789
100

Chromosome 3p Loss-Orchestrated VHL, HIF, and Epigenetic Deregulation in Clear Cell Renal Cell Carcinoma.
James J Hsieh, Valerie H Le, Toshinao Oyama, Christopher J Ricketts, Thai Huu Ho, Emily H Cheng. J Clin Oncol 2018
38
100

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.
Dvir Aran, Agnieszka P Looney, Leqian Liu, Esther Wu, Valerie Fong, Austin Hsu, Suzanna Chak, Ram P Naikawadi, Paul J Wolters, Adam R Abate,[...]. Nat Immunol 2019
341
100

A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue.
Flaminia Talos, Antonina Mitrofanova, Sarah K Bergren, Andrea Califano, Michael M Shen. Nat Commun 2017
16
100

Overexpression of TREM2 enhances glioma cell proliferation and invasion: a therapeutic target in human glioma.
Xiao-Qiang Wang, Bang-Bao Tao, Bin Li, Xu-Hui Wang, Wen-Chuan Zhang, Liang Wan, Xu-Ming Hua, Shi-Ting Li. Oncotarget 2016
30
100

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.
Aditya Dutta, Clémentine Le Magnen, Antonina Mitrofanova, Xuesong Ouyang, Andrea Califano, Cory Abate-Shen. Science 2016
51
100


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.